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Woei-Yuh Saw
I am currently a postdoctoral researcher at Baker Heart and Diabetes Institute in the System Genomics lab.
I have a strong interest in infer links with human complext traits by leveraging integrative multi-omics approaches into clinical environments to enable optimal data-supported decision making.
My academic research primarily explores genetic variation across global populations using multi-omics approaches and integrative omics for health and diseases.
Education
P.h.D
Saw Swee Hock School of Public Health
National University of Singapore
Singapore, SG
2019 - 2013
- Under supervison of Prof Yik-Ying Teo, Biostatistic and Modelling Domain
- Thesis title:“Mapping the natural variation of global populations”
B.Comp.
School of Computing
National University of Singapore
Singapore, SG
2011 - 2007
- Major in Computational Biology
Research Experience
Honorary Fellow
Baker Department of Cardiometabolic Health
University of Melbourne
Melbourne, AU
Today - 2021
- Collaborated with Dr Shu Mei Teo
- Explored polygenic risk prediction on cardiometabolic diseases and its related traits in non-European populations
- Performed polygenic risk scores calculation and compilation for cardiometabolic diseases, immune diseases, diseases-related traits using UK Biobank (UKB) dataset for in-house usage
Postdoctoral Research
System Genomics lab
Baker Heart and Diabetes Institute
Melbourne, AU
Today - 2019
- Under supervision of Prof Mike Inouye and Dr Shu Mei Teo (Senior Research fellow)
- Leading integrative omics projects using a longitudinal cohort (Childhood Asthma Study)
- Examined the extent of genetics of gene expressions in neonatal innate and adaptive immunity using genomics and transcriptomics data (manuscript in review by co-authors)
- Evaluated relationships between neonatal innate immune response and asthma related traits using genomics, transcriptomics, nasal 16S microbiota, and non-omics data (manuscript in review by co-authors)
- Contributed to the carbon footprint of bioinformatics tools project led by Dr Jason Grealey
Research Assistant
iOmics Programme
Life Sciences Institute
Singapore, SG
2019 - 2011
- Under supervison of Prof Yik-Ying Teo
- Experienced in managing and analysing multidisplinary research projects in and presented to both local and overseas collaborators
- Contributed and managed the development of iOmics (genomics, pharmacogenomics, HLA typing, transcriptomics, lipidomics, miRNAs, epigenomics - DNA methylation) and its extension, the Singapore Gut Microbiome Study
- Designed the study and wrote research protocol of The Singapore Gut Microbiome Study, although PIs conceived the idea to carry out research on the study
- Experienced in managing Logistics and Recruitment of participants for Singapore Integrative Omics Study (iOmics)
- Re-developed an open access decision tree builder for cost-effective assessment to a current tool called Plant-A-Tree®, version 1 (http://www.gear4health.com/page/i/plant-a-tree) using VBA
- Assisted PI in his milestone reports for grants and IRB
Internship
Computational biology lab
Genome Institute of Singapore
Singapore, SG
2010 - 2010
- Under supervision of A/P Niranjan Nagarajan
- Re-tooling a published research software – GiRaF: Influenza Reassortment Detection using C++ for in house usage
- Gained independent problem-solving skills in data processing and data analysis during the re-tooling process with C++
Teaching Experience
Student mentor
Saw Swee Hock School of Public Health
National University of Singapore
Singapore, SG
2019 - 2011
- Aided and supported students for their research projects
- 2 graduate students (Wai-Sum Yap and Chee-Wei Yew)on whole genome sequencing analysis and population genetics analysis
- 1 Master student (Melissa Butjor) on haplotype phasing for her downstream association with nutrients info analysis
- 2 undergraduate students (Kah-Yan Hoi and Evelyn Lim) on R programming for their epidemiological association analysis
NUS-MIT Healthcare Analytics Datathon
Saw Swee Hock School of Public Health
National University of Singapore
Singapore, SG
2017
- Student Lead for topic of “Identify potential clinical determinants in predicting outcome of patients who present to hospital with an Out-of-Hospital Cardiac Arrest” using MIMIC/EICU databases
Human Whole Genome Sequencing Data Analysis workshop
Biotechnology Research Institute
University Malaysia Sabah
Sabah, MY
2014
- Teaching assistant for whole genome sequencing analysis
Statistic for life sciences module - ST 1232
Department of Statistic and Applied Probability
National University of Singapore
Singapore, SG
2014
- Relief Teaching assistant during tutorial classes, when R programming is needed for statistical analysis
Service Experience
Recruiter
Saw Swee Hock School of Public Health
National University of Singapore
Singapore, SG
N/A
- Served on hiring committee for Research Assistant/Associate and participated in selection and interviewing processes
Skills and Training
Computational Tools
N/A
N/A
N/A
- Next-Gen sequencing analysis (GATK, BWA, samtools, Bowtie, BLAST, STAR, Picard, FastQC, cutadapt, TrimGalore, PennCNV, BirdSuite)
- Omics wide association analysis (PLINK, BOLT-LMM)
- Genomic Imputation and Phasing analysis (IMPUTE, minimac, Shapeit, Beagle, Eagle)
- Variant Annotation (SnpEff, Polyphen, SIFT, ANNOVAR)
- Gene expression and co-expression analysis (edgeR, WGCNA, DGCA)
- Functional annotation of pathways (DAVID, GSEA, Gorrila, enrichment R package)
- Evolutionary relationship analysis (Phylotree, MEGA, ADMIXTURE, PHYLIP)
- Microbiome profiling (MetaPhlAn version 1)
- Various R packages for statistical analysis
Programming languages
N/A
N/A
N/A
- R, Python, Perl, C++, Bash, Java, MySQL, HTML, VBA, Slurm, PBS, STATA commands
Certified standard Mental Health First Aider
Accredited by Mental Health First Aid Australia
Melbourne, AU
2024 - 2021
Scientific Communications
Using evidence to empower decisions: Health Technology Assessment
Health Intervention and Technology Assessment Program, Trainee
Singapore, SG
2019
Mapping the genetic diversity in cosmopolitan Malays and indigenous populations.
American Society of Human Genetics 2017 Annual Meeting, Poster
Orlando, USA
2017
Singapore Integrative Omics Cohort: Establishing multiple omics baseline for three Southeast Asian ethnic groups
American Society of Human Genetics 2016 Annual Meeting, Poster
Vancouver, CA
2016
Mapping the genetic diversity of HLA haplotypes in the Japanese populations
Japan Human Genetic Society 60th Conference, Poster
Tokyo, JPN
2015
Mapping the genetic diversity of HLA haplotype in Asia populations
American Society of Human Genetics 2012 Annual Meeting, Poster
San Francisco, USA
2012
Publications
Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative
Microbiology Spectrum, Read it here
N/A
2022
- Adrian Low,[…],Woei-Yuh Saw,[…], Yik Ying Teo, Niranjan Nagarajan, Henning Seedorf
Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians
BioRxiv, Read it here
N/A
2022
- Jean-Sebastien Gounot*, Chia Minghao*, Denis Bertrand*, Woei-Yuh Saw,[…], Teo Yik-Ying, Henning Seedorf, Niranjan Nagarajan
The Carbon Footprint of Bioinformatics
Molecular Biology and Evolution, Read it here
N/A
2022
- Jason Grealey*, Loïc Lannelongue*, Woei-Yuh Saw,[…], Michael Inouye
Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians
American Journal of Human Biology, Read it here
N/A
2021
- Jin Sun,[…],Woei-Yuh Saw,[…],Yik-Ying Teo,Hui Li
Genome-wide identification of cis DNA methylation quantitative trait loci in three Southeast Asian Populations
Human Molecular Genetics, Read it here
N/A
2021
- Irfahan Kassam,[…], Woei-Yuh Saw,[…], Yik-Ying Teo, Marie Loh
Extended-Spectrum β-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans
Applied and Environmental Microbiology, Read it here
N/A
2021
- Yichen Ding, Woei-Yuh Saw,[…], Niranjan Nagarajan, Yik Ying Teo, Henning Seedorf
Emergence of tigecycline- and eravacycline-resistant Tet(X4)-producing Enterobacteriaceae in the gut microbiota of healthy Singaporeans
Journal of Antimicrobial Chemotherapy, Read it here
N/A
2020
- Yichen Ding, Woei-Yuh Saw,[…], Niranjan Nagarajan, Yik Ying Teo, Henning Seedorf
Interethnic analyses of blood pressure loci in populations of East Asian and European descent
Nature Communications, Read it here
N/A
2018
- Fumihiko Takeuchi, Masato Akiyama,[…],Woei-Yuh Saw,[…], Michiaki Kubo & Norihiro Kato
Dataset on gene expression in the elderly after Mindfulness Awareness Practice or Health Education Program
Data in Brief, Read it here
N/A
2018
- Hwee-Woon Lim, Woei-Yuh Saw,[…], Ene-Choo Tan
Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error
Nature Genetics, Read it here
N/A
2018
- Milly S. Tedja, Robert Wojciechowski,[…],Woei-Yuh Saw,[…], Caroline C. W. Klaver
Phylogeography of Y-chromosome haplogroup O3a2b2-N6 reveals patrilineal traces of Austronesian populations on the eastern coastal regions of Asia
PLOS ONE, Read it here
N/A
2017
- Lan-Hai Wei ,Shi Yan ,[…],Woei-Yuh Saw,[…],Hui Li
The fine-scale genetic structure and evolution of the Japanese population
PLOS ONE, Read it here
N/A
2017
- Fumihiko Takeuchi ,[…],Woei-Yuh Saw,[…],Yik-Ying Teo ,Norihiro Kato
Establishing multiple omics baselines for three Southeast Asian populations in the Singapore Integrative Omics Study
Nature Communications, Read it here
N/A
2017
- Woei-Yuh Saw,[…],Yik-Ying Teo
Lipidomic profiling of plasma in a healthy Singaporean population to identify ethnic specific differences in lipid levels and associations with disease risk factors
Clinical Mass Spectometry, Read it here
N/A
2017
- Husna Begum,[…],Woei-Yuh Saw,[…],Markus R. Wenk
Dissecting the genetic structure and admixture of four geographical Malay populations
Scientific Reports, Read it here
N/A
2015
- Lian Deng,[…],Woei-Yuh Saw,[…], Yik-Ying Teo,Shuhua Xu
Differential positive selection of malaria resistance genes in three indigenous populations of Peninsular Malaysia
Human Genetics, Read it here
N/A
2015
- Xuanyao Liu,[…],Woei-Yuh Saw,[…], Yik-Ying Teo,Boon-Peng Hoh
Mapping the genetic diversity of HLA haplotypes in the Japanese populations
Scientific Reports, Read it here
N/A
2015
- Woei-Yuh Saw,[…], Yik-Ying Teo & Norihiro Kato
Predicting HLA alleles from high-resolution SNP data in three Southeast Asian populations
Scientific Reports, Read it here
N/A
2014
- Nisha Esakimuthu Pillai, Yukinori Okada,Woei-Yuh Saw,[…], Paul I. W. De Bakker, Yik-Ying Teo
Evaluating the possibility of detecting evidence of positive selection across Asia with sparse genotype data from the HUGO Pan-Asian SNP Consortium
BMC Genomics, Read it here
N/A
2014
- Xuanyao Liu,Woei-Yuh Saw,[…],Yik-Ying Teo
Evaluating the coverage and potential of imputing the exome microarray with next-generation imputation using the 1000 Genomes Project
PLOS ONE, Read it here
N/A
2014
- Erwin Tantoso,[…],Woei-Yuh Saw,[…],Yik-Ying Teo
Insights into the genetic structure and diversity of 38 South Asian Indians from deep whole-genome sequencing
PLOS Genetics, Read it here
N/A
2014
- Lai-Ping Wong ,Jason Kuan-Han Lai ,Woei-Yuh Saw,[…],Yik-Ying Teo
The HLA-DRβ1 amino acid positions 11-13-26 explain the majority of SLE-MHC associations
Nature Communications, Read it here
N/A
2014
- Kwangwoo Kim,[…],Woei-Yuh Saw, Yik-Ying Teo, Sang-Cheol Bae